tbuckley/cabot-search huggingface dataset:
RNA interference screens discover proteases as synthetic lethal partners of PI3K inhibition in breast cancer cells
Authors: Lena Hölzen, Jan Mitschke, Claudia Schönichen, Maria Elena Hess, Sophia Ehrenfeld, Melanie Boerries, Cornelius Miething, Tilman Brummer, Thomas Reinheckel
Journal: Theranostics (2022)

Rationale: PI3K/mTOR signaling is frequently upregulated in breast cancer making inhibitors of this pathway highly promising anticancer drugs.However, PI3K-inhibitors have a low therapeutic index.Therefore, finding novel combinatory treatment options represents an important step towards clinical implementation of PI3K pathway inhibition in breast cancer therapy.Here, we propose proteases as potential synergistic partners with simultaneous PI3K inhibition in breast cancer cells.Methods: We performed mRNA expression studies and unbiased functional genetic synthetic lethality screens by a miR-E based knockdown system targeting all genome-encoded proteases, i.e. the degradome of breast cancer cells.Importantly theses RNA interference screens were done in combination with two PI3K pathway inhibitors.Protease hits were validated in human and murine breast cancer cell lines as well as in non-cancerous cells by viability and growth assays.Results: The degradome-wide genetic screens identified 181 proteases that influenced susceptibility of murine breast cancer cells to low dose PI3K inhibition.Employing independently generated inducible knockdown cell lines we validated 12 protease hits in breast cancer cells.In line with the known tumor promoting function of these proteases we demonstrated Usp7 and Metap2 to be important for murine and human breast cancer cell growth and discovered a role for Metap1 in this context.Most importantly, we demonstrated that Usp7, Metap1 or Metap2 knockdown combined with simultaneous PI3K inhibition resulted in synergistic impairment of murine and human breast cancer cell growth Conclusion: We successfully established proteases as combinatory targets with PI3K inhibition in human and murine breast cancer cells.Usp7, Metap1 and Metap2 are synthetic lethal partners of simultaneous protease/PI3K inhibition, which may refine future breast cancer therapy.
Evaluation of cancer immunotherapy using mini-tumor chips
Authors: Zheng Ao, Hongwei Cai, Zhuhao Wu, Liya Hu, Xiang Li, Connor Kaurich, Mingxia Gu, Liang Cheng, Xin Lu, Feng Guo
Journal: Theranostics (2022)

Rationale: Predicting tumor responses to adjuvant therapies can potentially help guide treatment decisions and improve patient survival.Currently, tumor pathology, histology, and molecular profiles are being integrated into personalized profiles to guide therapeutic decisions.However, it remains a grand challenge to evaluate tumor responses to immunotherapy for personalized medicine.Methods: We present a microfluidics-based mini-tumor chip approach to predict tumor responses to cancer immunotherapy in a preclinical model.By uniformly infusing dissociated tumor cells into isolated microfluidic well-arrays, 960 mini-tumors could be uniformly generated on-chip, with each well representing the ex vivo tumor niche that preserves the original tumor cell composition and dynamic cell-cell interactions and autocrine/paracrine cytokines.Results: By incorporating time-lapse live-cell imaging, our mini-tumor chip allows the investigation of dynamic immune-tumor interactions as well as their responses to cancer immunotherapy (e.g., anti-PD1 treatment) in parallel within 36 hours.Additionally, by establishing orthotopic breast tumor models with constitutive differential PD-L1 expression levels, we showed that the on-chip interrogation of the primary tumor's responses to anti-PD1 as early as 10 days post tumor inoculation could predict the in vivo tumors' responses to anti-PD1 at the endpoint of day 24.We also demonstrated the application of this mini-tumor chip to interrogate on-chip responses of primary tumor cells isolated from primary human breast and renal tumor tissues.Conclusions: Our approach provides a simple, quick-turnaround solution to measure tumor responses to cancer immunotherapy.
APOBEC-mediated mutagenesis is a favorable predictor of prognosis and immunotherapy for bladder cancer patients: evidence from pan-cancer analysis and multiple databases
Authors: Run Shi, Xin Wang, Yang Wu, Bin Xu, Tianyu Zhao, Christian Trapp, Xuanbin Wang, Kristian Unger, Cheng Zhou, Shun Lu, Alexander Buchner, Gerald Bastian Schulz, Fengjun Cao, Claus Belka, Chuan Su, Minglun Li, Yongqian Shu
Journal: Theranostics (2022)

Background: The APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) family-mediated mutagenesis is widespread in human cancers. However, our knowledge of the biological feature and clinical relevance of APOBECs and APOBEC mutagenesis in cancers remains limited. Methods: In this study, with a series of bioinformatic and statistical approaches, we performed a comprehensive analysis of multiple levels of data, including whole-exome sequencing (WES) and targeted next-generation sequencing (NGS), transcriptome (bulk RNA-seq and single-cell RNA-seq), immune signatures and immune checkpoint blockade (ICB) potential, patient survival and drug sensitivity, to reveal the distribution characteristics and clinical significance of APOBECs and APOBEC mutagenesis in pan-cancer especially bladder cancer (BLCA). Results: APOBEC mutagenesis dominates in the mutational patterns of BLCA. A higher enrichment score of APOBEC mutagenesis correlates with favorable prognosis, immune activation and potential ICB response in BLCA patients. APOBEC3A and 3B play a significant role in the malignant progression and cell differentiation within the tumor microenvironment. Furthermore, using machine learning approaches, a prognostic APOBEC mutagenesis-related model was established and validated in different BLCA cohorts. Conclusions: Our study illustrates the characterization of APOBECs and APOBEC mutagenesis in multiple cancer types and highlights its potential value as a promising biomarker for prognosis and immunotherapy in BLCA.
Arterial cyclic stretch regulates Lamtor1 and promotes neointimal hyperplasia via circSlc8a1/miR-20a-5p axis in vein grafts
Authors: Ji-Ting Liu, Qing-Ping Yao, Yi Chen, Fan Lv, Ze Liu, Han Bao, Yue Han, Ming-Liang Zhang, Zong-Lai Jiang, Ying-Xin Qi
Journal: Theranostics (2022)

Rationale: Neointimal hyperplasia caused by dedifferentiation and proliferation of venous smooth muscle cells (SMCs) is the major challenge for restenosis after coronary artery bypass graft.Herein, we investigated the role of Lamtor1 in neointimal formation and the regulatory mechanism of non-coding RNA underlying this process.Methods: Using a "cuff" model, veins were grafted into arterial system and Lamtor1 expression which was correlated with the activation of mTORC1 signaling and dedifferentiation of SMCs, were measured by Western blot.Whole transcriptome deep sequencing (RNA-seq) of the grafted veins combined with bioinformatic analysis identified highly conserved circSlc8a1 and its interaction with miR-20a-5p, which may target Lamtor1.CircSlc8a1 was biochemically characterized by Sanger sequencing and resistant to RNase R digestion.The cytoplasmic location of circSlc8a1 was shown by fluorescence in situ hybridization (FISH).RNA pull-down, luciferase assays and RNA immunoprecipitation (RIP) with Ago2 assays were used to identify the interaction circSlc8a1 with miR-20a-5p.Furthermore, arterial mechanical stretch (10% elongation) was applied in vitro.Results: In vivo, Lamtor1 was significantly enhanced in grafted vein and activated mTORC1 signaling to promote dedifferentiation of SMCs.Arterial mechanical stretch (10% elongation) induced circSlc8a1 expression and positively regulated Lamtor1, activated mTORC1 and promoted SMC dedifferentiation and proliferation.Local injection of circSlc8a1 siRNA or SMC-specific Lamtor1 knockout mice prevented neointimal hyperplasia in vein grafts in vivo.Conclusions: Our study reveals a novel mechanobiological mechanism underlying the dedifferentiation and proliferation of venous SMCs in neointimal hyperplasia.CircSlc81/miR-20a-5p/Lamtor1 axis induced by arterial cyclic stretch may be a potential clinical target that attenuates neointimal hyperplasia in grafted vessels.
M2 microglia-derived extracellular vesicles promote white matter repair and functional recovery via miR-23a-5p after cerebral ischemia in mice
Authors: Yongfang Li, Ze Liu, Yaying Song, Jia-ji Pan, Yixu Jiang, Xiaojing Shi, Chang Liu, Yuanyuan Ma, Longlong Luo, Muyassar Mamtilahun, Zhiyu Shi, Haroon Khan, Qing Xie, Yongting Wang, Yaohui Tang, Zhijun Zhang, Guo-Yuan Yang
Journal: Theranostics (2022)

Rationale: White matter repair is critical for the cognitive and neurological functional recovery after ischemic stroke.M2 microglia are well-documented to enhance remyelination and their extracellular vesicles (EVs) mediate cellular function after brain injury.However, whether M2 microglia-derived EVs could promote white matter repair after cerebral ischemia and its underlying mechanism are largely unknown.Methods: EVs were isolated from IL-4 treated microglia (M2-EVs) and untreated microglia (M0-EVs).Adult ICR mice subjected to 90-minute transient middle cerebral artery occlusion received intravenous EVs treatment for seven consecutive days.Brain atrophy volume, neurobehavioral tests were examined within 28 days following ischemia.Immunohistochemistry, myelin transmission electron microscope and compound action potential measurement were performed to assess white matter structural remodeling, functional repair and oligodendrogenesis.The effects of M2-EVs on oligodendrocyte precursor cells (OPCs) were also examined in vitro.EVs' miRNA sequencing, specific miR-23a-5p knockdown in M2-EVs and luciferase reporter assay were used to explore the underlying mechanism.Results: M2-EVs reduced brain atrophy volume, promoted functional recovery, oligodendrogenesis and white matter repair in vivo, increased OPC proliferation, survival and differentiation in vitro.miR-23a-5p was enriched in M2-EVs and could promote OPC proliferation, survival and maturation, while knocking down miR-23a-5p in M2-EVs reversed the beneficial effects of M2-EVs both in vitro and in vivo.Luciferase reporter assay showed that miR-23a-5p directly targeted Olig3.Conclusion: Our results demonstrated that M2 microglia could communicate to OPCs through M2-EVs and promote white matter repair via miR-23a-5p possibly by directly targeting Olig3 after ischemic stroke, suggesting M2-EVs is a novel and promising therapeutic strategy for white matter repair in stroke and demyelinating disease.
Highly elastic 3D-printed gelatin/HA/placental-extract scaffolds for bone tissue engineering
Authors: JiUn Lee, Dongyun Kim, Chul Ho Jang, Geun Hyung Kim
Journal: Theranostics (2022)

Bioengineering scaffolds have been improved to achieve efficient regeneration of various damaged tissues.In this study, we attempted to fabricate mechanically and biologically activated 3D printed scaffold in which porous gelatin/hydroxyapatite (G/H) as a matrix material provided outstanding mechanical properties with recoverable behavior, and human placental extracts (hPE) embedded in the scaffold were used as bioactive components.Methods: Various cell types (human adipose-derived stem cells; hASCs, pre-osteoblast; MC3T3-E1, human endothelial cell line; EA.hy926, and human dermal fibroblast; hDFs) were used to assess the effect of the hPE on cellular responses.High weight fraction (~ 70 wt%) of hydroxyapatite (HA) in a gelatin solution supplemented with glycerol was used for the G/H scaffold fabrication, and the scaffolds were immersed in hPE for the embedding (G/H/hPE scaffold).The osteogenic abilities of the scaffolds were investigated in cultured cells (hASCs) assaying for ALP activity and expression of osteogenic genes.For the in vivo test, the G/H and G/H/hPE scaffolds were implanted in the rat mastoid obliteration model. Results:The G/H/hPE scaffold presented unique elastic recoverable properties, which are important for efficient usage of implantable scaffolds.The effects of G/H and G/H/hPE scaffold on various in vitro cell-activities including non-toxicity, biocompatibility, and cell proliferation were investigated.The in vitro results indicated that proliferation (G/H = 351.1 ± 13.3%, G/H/hPE = 430.9± 8.7% at day 14) and expression of osteogenic markers (ALP: 3.4-fold, Runx2: 3.9-fold, BMP2: 1.7-fold, OPN: 2.4-fold, and OCN: 4.8-fold at day 21) of hASCs grown in the G/H/hPE scaffold were significantly enhanced compared with that in cells grown in the G/H scaffold.In addition, bone formation was also observed in an in vivo model using rat mastoid obliteration. Conclusion:In vitro and in vivo results suggested that the G/H/hPE scaffold is a potential candidate for use in bone tissue engineering.
Accurate programmed multifunctional nano-missiles for self-promoted deep delivery and synergistic cascade tumor therapy: Tactfully collaborating chemosynthesis with tumor microenvironment remodeling
Authors: Runxin Lu, Siqi Wang, Zhongzhen Yang, Lin Zhou, Chunyan Yang, Yong Wu
Journal: Theranostics (2022)

Triple-negative breast cancer (TNBC) is considered one of the highest-risk subtypes of breast cancer and has dismal prognosis. The management of aggressive TNBC remains a formidable challenge. Tumor microenvironment (TME), with the unique features, which can serve as the "soil" for the growth and survival of tumor cells (the "seeds"), plays an important regulatory role in the occurrence, proliferation and metastasis of tumors. Catalytic tumor therapy, which can destroy the homeostasis of TME, affect the occurrence and progress of tumors in an all-round way and further magnify chemotherapy, is a quite potential tactic for TNBC-treatment.
Fibroblast activation protein α activatable theranostic pro-photosensitizer for accurate tumor imaging and highly-specific photodynamic therapy
Authors: Yong Luo, Zishan Zeng, Ting Shan, Xiaoyu Xu, Jie Chen, Yuanfeng He, Tao Zhang, Zeqian Huang, Guihong Chai, Yanjuan Huang, Yanfang Zhao, Chunshun Zhao
Journal: Theranostics (2022)

The development of activatable photosensitizers (aPSs) responding to tumor-specific biomarkers for precision photodynamic therapy (PDT) is urgently required. Due to the unique proteolytic activity and highly restricted distribution of tumor-specific enzymes, enzyme activatable photosensitizers display superior selectivity.
Cathelicidin-related antimicrobial peptide protects against enteric pathogen-accelerated type 1 diabetes in mice
Authors: Lingling Jia, Jiahong Li, Ming Zhang, He Liu, Zhengnan Ren, Xiao Liang Dong, Xiaohua Pan, Ju Qiu, Li-Long Pan, Jia Sun
Journal: Theranostics (2022)

Rationale: Gut barrier disruption caused by enteric pathogen infection results in activated diabetogenic T cells and accelerated type 1 diabetes (T1D).Cathelicidin-related antimicrobial peptide (CRAMP) maintains intestinal barrier integrity, regulates the microbiome, and exerts positive immune-modulatory effects on pancreatic diseases.Methods: The model enteric pathogen Citrobacter rodentium (C.rodentium) was adopted to represent clinical colonic infection with gut barrier disruption.The protective role and gut-pancreas pathophysiological mechanism of CRAMP in enteric pathogen-accelerated T1D were investigated in spontaneous non-obese diabetic (NOD) mice and streptozotocin-induced diabetic mice.Results: Colonic CRAMP production was defective in C. rodentium infection-accelerated T1D. C. rodentium infection triggered the recruitment of interferon-gamma (IFN-γ) + T cells and accelerated T1D.In the C. rodentium-accelerated T1D mice, CRAMP deficiency further aggravated gut barrier disruption, gut dysbiosis, and diabetic phenotype, which could be reversed by CRAMP treatment.The protective effect of CRAMP may be due to CRAMP inhibiting C. rodentium-aggravated gut immune dysregulation, gut dysbiosis, and migration of gut-primed IFN-γ + T cells to the pancreas, thus contributing to gut barrier protection and pancreatic-intestinal immune homeostasis.Conclusion: CRAMP plays a pivotal role in pancreatic-gut crosstalk during C. rodentium-accelerated T1D by gut barrier-protective, immune-and microbial-modulatory mechanisms.Cathelicidin supplementation to restore a healthy gut barrier may represent a novel therapeutic strategy for T1D.
SCD1/FADS2 fatty acid desaturases equipoise lipid metabolic activity and redox-driven ferroptosis in ascites-derived ovarian cancer cells
Authors: Yang Xuan, Huogang Wang, Mingo MH Yung, Fushun Chen, Wai-Sun Chan, Yau-Sang Chan, Stephen KW Tsui, Hextan YS Ngan, Karen KL Chan, David W Chan
Journal: Theranostics (2022)

Rationale: Malignant ascites in peritoneal metastases is a lipid-enriched microenvironment and is frequently involved in the poor prognosis of epithelial ovarian cancer (EOC). However, the detailed mechanisms underlying ovarian cancer (OvCa) cells dictating their lipid metabolic activities in promoting tumor progression remain elusive. Methods: The omental conditioned medium (OCM) was established to imitate the omental or ascites microenvironment. Mass spectrometry, RT-qPCR, IHC, and western blot assays were applied to evaluate human fatty acid desaturases expressions and activities. Pharmaceutical inhibition and genetic ablation of SCD1/FADS2 were performed to observe the oncogenic capacities. RNA sequencing, lipid peroxidation, cellular iron, ROS, and Mito-Stress assays were applied to examine ferroptosis. OvCa patient-derived organoid and mouse model of peritoneal metastases were used to evaluate the combined effect of SCD1/FADS2 inhibitors with cisplatin. Results: We found that two critical fatty acid desaturases, stearoyl-CoA desaturase-1 (SCD1) and acyl-CoA 6-desaturase (FADS2), were aberrantly upregulated, accelerating lipid metabolic activities and tumor aggressiveness of ascites-derived OvCa cells. Lipidomic analysis revealed that the elevation of unsaturated fatty acids (UFAs) was positively associated with SCD1/FADS2 levels and the oncogenic capacities of OvCa cells. In contrast, pharmaceutical inhibition and genetic ablation of SCD1/FADS2 retarded tumor growth, cancer stem cell (CSC) formation and reduced platinum resistance. Inhibition of SCD1/FADS2 directly downregulated GPX4 and the GSH/GSSG ratio, causing disruption of the cellular/mitochondrial redox balance and subsequently, iron-mediated lipid peroxidation and mitochondrial dysfunction in ascites-derived OvCa cells. Conclusions: Combinational treatment with SCD1/FADS2 inhibitors and cisplatin synergistically repressed tumor cell dissemination, providing a promising chemotherapeutic strategy against EOC peritoneal metastases.
CRISPR-Cas9 library screening approach for anti-cancer drug discovery: overview and perspectives
Authors: Yau-Tuen Chan, Yuanjun Lu, Junyu Wu, Cheng Zhang, Hor-Yue Tan, Zhao-xiang Bian, Ning Wang, Yibin Feng
Journal: Theranostics (2022)

CRISPR-Cas9 is a Nobel Prize-winning robust gene-editing tool developed in the last decade. This technique enables a stable genetic engineering method with high precision on the genomes of all organisms. The latest advances in the technology include a genome library screening approach, which can detect survival-essential and drug resistance genes via gain or loss of function. The versatile machinery allows genomic screening for gene activation or inhibition, and targets non-coding sequences, such as promoters, miRNAs, and lncRNAs. In this review, we introduce the emerging high-throughput CRISPR-Cas9 library genome screening technology and its working principles to detect survival and drug resistance genes through positive and negative selection. The technology is compared with other existing approaches while focusing on the advantages of its variable applications in anti-cancer drug discovery, including functions and target identification, non-coding RNA information, actions of small molecules, and drug target discoveries. The combination of the CRISPR-Cas9 system with multi-omic platforms represents a dynamic field expected to advance anti-cancer drug discovery and precision medicine in the clinic.
Grafted human ESC-derived astroglia repair spinal cord injury via activation of host anti-inflammatory microglia in the lesion area
Authors: Jian Wang, Peng Jiang, Wenbin Deng, Yuhui Sun, Yaobo Liu
Journal: Theranostics (2022)

Grafted astroglia/astrocytes exhibit neuroprotective effects and improve functional recovery after injury to the central nervous system.This study sought to elucidate their ability to repair spinal cord lesions and the underlying mechanisms.Methods: Complete spinal transection, transplantation of astroglia generated from human ESC-derived neural progenitor cells (NPC-Astros) or Olig2-GFP knock-in progenitors (Olig2PC-Astros), and immunostaining were used to determine the survival of astroglia.CUBIC tissue-clearing, immunostaining, electromyography, and functional tests such as the Basso Mouse Scale score and gait analysis were applied to analyze the recovery of the lesion area, axon regeneration, synapse formation, and motor function.Sholl analysis, immunostaining, depletion of anti-inflammatory microglia, and western blotting were employed to explore the cellular and molecular mechanisms underlying spinal cord repair.Results: Grafted NPC-or Olig2PC-Astros survived in the lesion area and assisted wound healing by reducing scar formation and promoting regrowth of descending serotonergic axons and synapse reformation beyond the lesion area.These positive effects resulted in increased Basso Mouse Scale scores and improved hindlimb function as determined by electromyography and gait analysis.Activated microglia in the lesion area were shifted towards an anti-inflammatory phenotype after transplantation of NPC-or Olig2PC-Astros, and depletion of anti-inflammatory microglia reversed the observed improvements in the lesion area and axon regeneration.Transplantation of NPC-or Olig2PC-Astros elevated the expression of interleukin-4 and promoted the phenotypic shift of microglial via interleukin-4 downstream signaling. Conclusion:Our findings indicate that grafted human ESC-derived NPC-or Olig2PC-Astros promote recovery of the injured spinal cord by shifting microglia towards an anti-inflammatory state in the lesion area and activating interleukin-4 signaling.